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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg...

Basic information

species Vitis vinifera
transcript Vv11s0052g01840.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G073380_T01 (Zea mays), 5'ss of exon 4
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtt---taacttgtcaaatgacacagtggtgcttacatatgtttcaatta-tgtatatgtgtg-tatgtgtgtgtattttccttt-tgtttgtagtcaactg----------------------
|||||||||||| ||||| || |||||||| |  |||| |||||||||| | || ||||| ||| ||||||| || |||||||| || || ||||   |||    | |  |||| || |  |     ||  ||  | |||||   |  |  | || ||     ||  | || | ||  |     | |||  |||                      
TGTGAGGGCAATCGTTGCATTAAATCTTCACAATTATGCAAGTGGAAGAAACCCTTGGGGAAATTTGAAGCCTGAATATTTGGAGAAAgtgtgttgagtaaaaatttatgtgac-cattcatcacctcaattgcattaattaacattgacttctgataaactcgttcaattgcattaattaacattgtcttctgataaactcgtttatgtcaatag

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA13G01360.2 (Glycine max), 5'ss of exon 10
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtt-----------taacttgtcaa-atgacacagtggtgctta--catatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg------------------------------------------------------------------------
||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| |  || ||||| |||||||||||||||||||           || ||  | ||  ||| |     |   | |  |  ||||| || |||| ||||      |||  |  | | | |  ||     |   ||  ||||                                                                         
TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAGgtatgttgcctaagataatacctcattaatgtgatatgaaagcattcaatctcatgttccatttatttataaaaaaatatagggat-tgtatagctgaaaatataagctaactaacttgatgaaactgttagtgttattcaaatttgatcatgattgactgaatagacttattggtgtacttccag

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA17G07480.1 (Glycine max), 5'ss of exon 10
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgt-----ttcaatt--atgt-------atatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg-----------------------------------------------------------------------------------
||| |||||||||||||||||||| |||||||||||||||||||||||| ||||||||||||| |  || ||||| |||||||||||||||||||   ||     ||| || || || ||     |||||      ||||||   ||||       || | | |  |    | |     | | | |||| | |||   | |                                                                                    
TGTAAGGGCAATAGTTGCTTTGAACCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGATTATTTGGAAAAGgtatgtt-gcctaacataataactcattgatgtgatgatatgaaagcattcaatctcatgttccttctatttttttaaaaaaatctagggatacatattgtgtatagctgaatataagctaactaacttgatgaaactgttagtgttattcaaatttaatcatgattgactgaatggacttattggtgtacttccag

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G30040.1 (Glycine max), 5'ss of exon 3
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatat-gtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg-
||| || |||||||||||| | ||||||||||| ||||||||||||||| |||||||||||||| |||  || || ||||| || |||||||  |    |  |   || |  |  ||     || ||   |   | |  | |||||       ||  | |   | |   |    |   | ||     |  
TGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAGgtatactct-ttcctttgataattctatgagatcta-atggttgaaagtattctatattacaatgataggggaaaaatacacaagagaagggagcatggttt

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA18G22370.1 (Glycine max), 5'ss of exon 3
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtat--gtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg
||| || |||||||||||| | || |||||||| ||||||||||||||| |||||||||||||| | |  || || ||||| || |||||||     ||  || ||   ||| |      ||   |   ||| || ||     ||||| |    ||      | |   | |    |    |     |   
TGTAAGAGCAATAGTTGCTCTAAACCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTAACACCTGAGTATTTAGAGAAGgtattgaactactttttcctttgataattctatgtgcattgatggttgaaagtattatatattacaataataaggaaaaatacacaagagaatgaagcat--

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT4G30340.1 (Arabidopsis thaliana), 5'ss of exon 7
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg
 || ||  | || || |  ||||||||| ||| ||||||||||||||||||||||||||||||||| |  ||| | ||||| || ||||||    |||  | | |      ||| |  | ||||  | |  ||   || | || | |  |  |   |   || ||    |||| |    ||       
CGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAGgtaa---taatgttttattcagtacactaat-cttaggttttattgctttctctacaagctttaaca-gaacgtgttcgggttttata-acag-------

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT2G18730.1 (Arabidopsis thaliana), 5'ss of exon 10
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgt-ttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg
||||||  |||| || || ||||||||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||| | || |||||||  ||    |||   ||  ||         | | |||||   ||| || | |  ||||      |  ||| |  |||  ||||  |            
TGTGAGATCAATTGTCGCATTGAATCTTCACAGCTATGGAAGTGGAAGCCATCCTTGGGGCAATCTAAAACCGGACTATCTAGAGAAGgtattgtt--tctgttccatttca---------tcatatatgaactcagttctctg-atgttaacccgaatgttttctttggtttttctcag---------

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 5'ss of exon 8
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg
||| || ||| | ||||| |||||||| ||||||||||||||||||||| | || ||||| ||||| || | ||| ||| | ||||| |||     ||  |        |     | ||   | || |  | | | ||||  ||     |   | |    |  |  |  | ||||  |||        
TGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAAgtaaaacaaagctc-------attttttcgtcacttcacaaatct-acttatcaattctccttcttattaacggttgcttgtgttgtacgtaacag----

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110400722|gb|EC967297.1|EC967297
EST:     GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG                         AAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
genomic: GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaa ... tacttttcagAAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
EST: gi|30303616|gb|CB980410.1|CB980410
EST:     GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG                         AAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
genomic: GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaa ... tacttttcagAAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
EST: gi|30304336|gb|CB981130.1|CB981130
EST:     GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG                         AAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
genomic: GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaa ... tacttttcagAAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
EST: gi|26266030|gb|CA817093.1|CA817093
EST:     GGGGTAATCTGAAGCCAGACTATTTGGAAAAG                         AAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
genomic: GGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaa ... tacttttcagAAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
EST: gi|83276057|gb|DV940065.1|DV940065
EST:     GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG                         AAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC
genomic: GAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaa ... tacttttcagAAAGGTTTTGTTGAGGCTCATGTCGATGATGGGCTTCTAGAAATTTTTGGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGgtatgtttaacttgtcaaatgacacagtggtgcttacatatgtttcaattatgtatatgtgtgtatgtgtgtgtattttccttttgtttgtagtcaactg

- - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaca